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Replacing headers based on a second file

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# 1  
Old 07-28-2011
Replacing headers based on a second file
I have a file with thousands of sequences that looks like this:
Quote:
>SeqID1
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Sequence 22
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Seq-39
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
I need to replace the headers using a second file
Quote:
HIV
WNV
Flu
Thus, I will end up having the following file:
Quote:
>HIV
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>WNV
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
>Flu
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
I am looking for an AWK script that I can easily plug in my current pipeline.
Any help will be greatly appreciated!
# 2  
Old 07-28-2011
Hi Xterra Smilie Try this:
Code:
awk 'NR==FNR{a[NR]=$0;next}FNR%2{$0=">"a[int(FNR/2+1)]}1' file2 file1

Last edited by bartus11; 07-28-2011 at 02:50 PM..
This User Gave Thanks to bartus11 For This Post:
Xterra
# 3  
Old 07-28-2011
This will work:
Code:
#!/usr/bin/ksh
sed -n 's/^>\(.*\)/s#>\1#/p' Large_File > Tmp1
paste -d'>' Tmp1 String_File > Tmp2
sed 's/$/#/' Tmp2 > Sed_File
sed -f Sed_File Large_File

# 4  
Old 07-28-2011
bartus11
As usual, a great solution!
Thank you very, very much!
# 5  
Old 07-28-2011
Code:
awk '/>/ {getline a<"file2";$0=">" a}1' file1

This User Gave Thanks to rdcwayx For This Post:
Xterra
# 6  
Old 07-29-2011
Yet another approach:
Code:
paste -d\\n file1 <(sed G file2) | sed -n 'n; N; p; n'

Regards,
Alister
# 7  
Old 07-29-2011
rdcwayx
Very nice!
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